The development and availability of improved vaccines, particularly the pneumococcal (PCV) and Haemophilus influenzae type b (Hib) conjugate vaccines have substantially reduced the incidence of childhood pneumonia and severe pneumonia associated with these pathogens over the last decade. However, despite a declining pneumonia incidence and high rates of immunisation, pneumonia remains the leading cause of childhood mortality globally and a major cause of hospitalisation.

Defining the aetiology of pneumonia has become crucial to develop appropriate management strategies, and guide development of new vaccines. Further, the development of better methods for specimen collection and of molecular diagnostics has provided more sensitive techniques to define potential aetiological agents.

However, assigning aetiology may be challenging as it can be difficult to distinguish colonising from pathogenic organisms in respiratory specimens, blood culture rarely is positive and pneumonia, especially severe disease, may frequently be due to multiple copathogens....